Mass Effect 2: Shepard Commander
by Blarghums
Summary: Alternate beginning rumor, Geth picked up Shepard's body instead of Cerberus. Legion has numerous lines that hint at an alternate script that was later dropped. I found that scenario more interesting and decided to explore it. *dropped*
1. Chapter 1

**Disclaimer**

All characters belong to their respective copyright holders, i do not own yadda yadda, i'm actually not sure what goes into one of these, could use some help on that front

**A/N**

First attempt at this kind of thing, be kind yet fair if you are going to review, i'm not sure how i take criticism but i'd prefer you be honest. Anyway, i'm not sure where i want to go with this but i think i'd probably enjoy continuing it. If there are any errors i'd like to fix them, i'll throw an edit point to let people know what's been changed if i ever do change them at the end of each chapter?

**Normandy**** Cockpit**

"Ow, watch the arm." Joker shouted as Shepard hauled him out of the pilot seat.

"If you don't hurry your ass up…" Shepard's threat left off as he turned his head and noticed the shadow of the rapidly approaching enemy vessel race across the gaping hole in the Normandy's hull. Silently, Shepard threw the fragile pilot's already abused arm over his shoulder causing Joker to wince slightly. Ninety percent carrying, ten percent assisting, Shepard helped Joker make their way to the cockpit escape shuttle.

Shoving Joker hastily into the closest empty seat Shepard noticed the slight widening of Joker's eyes as he looked passed Shepard's shoulder. Shepard turned to find a column of blinding energy sweeping through what had been the bridge of his ship. Suddenly, Shepard felt his body rocked by an explosion to his left. The beam had swept through a nearby fire extinguisher, instantaneously super-heating its contents.

Shepard's vision started to clear moments after the explosion. As he careened off the wall the blast had sent him into he thought wryly,_ "Done in by a fire extinguisher, perfect."_ With one last look at Joker, who was desperately trying to scramble out of the seat in the still-waiting escape pod, Shepard reached out and hit the eject button that was attached to the rapidly receding wall of the rapidly receding wreck of his vessel.

As Shepard busily tried to think of some way out of his predicament, spaced with no idea of how long help would take, he noticed a hissing sound emanating from his suit. Shepard scrambled to reattach the hose that had most likely come loose from the earlier impact when the futility of his situation dawned on him. As he watched the pressure reading on his suit rapidly fall toward zero the enemy ship lazily spun into view. Getting his first good look at his killers just before they jumped away he thought to himself:

_"Perfect, spaced by a giant flying turd and a fire extinguisher; soon to suffocate and burn to a crisp in the atmosphere of some backwater planet, why can't I stop thinking about Tali's hips?"_

As his vision slowly darkened Shepard couldn't help wondering two last things:

_"How would Tali feel in my arms?"_ and _"What the hell is that Geth scout-ship doing here?"_

…

**Citadel Docks**

_Thing one of seven makes sounds_

_Thing two of seven makes short regular sounds, decreases in height_

_Thing three moves to Thing two_

_Thing four moves to Thing five_

_Thing five is broken_

_Thing six hits barrier with extremity_

_Thing seven leaves cluster_

***

_They scour the wreckage of the __Normandy__ but the locator beacon in Shepard's suit is not broadcasting, Shepard's body is believed to have been vaporized on its entry into the atmosphere of the planet._

_Two weeks after the attack on the __Normandy__ the search for the remains of Commander Shepard, Hero of the __Alliance__ and Savior of the Citadel officially ends._

_All they've found are a charred and rent N7 Helmet and a single scorched shoulder pad._

***

_Pilot relays account to what's left of traumatized crew of __Normandy__. _

_Sobbing fills air_

_Turian moves to console Quarian_

_Human lays hand on shoulder of stunned Asari_

_Krogan dents wall with fist_

_Human turns and walks away_

***

_They hold a memorial for Shepard in the Presidium, the new Council presents Shepard's orphanage with the Citadel's highest honor, the Archetype Star, awarded to those whom represent those traits held in highest esteem: Discipline, Compassion, Wit, Fortitude and Flexibility. Alliance opens charity in Shepard's name, his date of birth has been lost, they declare his naval enrollment day an terrestrial holiday. __Anderson__ delivers a stirring eulogy. Udina looks upset, though it may just be impatience at having to attend._

***

_Joker, barely audible, relays his account of his final moments aboard the __Normandy__. He pauses midway through and takes a moment to compose himself before finishing._

_Silence takes over for a brief second as the news sinks in, each person reacts differently:_

_Tali sinks to her knees and starts sobbing, it's a heartbreaking sound, an endless unbroken line of muffled and choked cries; she must've turned off her comm system._

_Anderson__ looks shocked and saddened and resolute. He quickly leaves to grieve in private and attend to the necessary matters. He will not let anyone else do this._

_Liara looks stunned and speechless. Kaidan lays a hand on her shoulder and she flinches, her face darkens. She storms off, Kaidan asks her where she's going, she throws out "to get some answers."_

_Wrex begins to look increasingly agitated until he throws back his head, lets loose a roar, and hits the side of the transport shuttle hard enough to leave a dent. He leaves with only "this was not worthy of him." I would have to agree… _waitwhat_?_

_Garrus sits next to Tali to show his support, she throws her arms around him hiding her face against his armor. He awkwardly wraps an arm around her and pats her on the back. I'll have to thank him for th… _hrm… this isn't my memo-

**No, this is not your memory, this is a recording**

Holy crap, what the fuck, What the fuck!? why is there another voice in my head, why is there a head, why am I alive, am I alive, what the fu-

**We will answer your questions, but first _*Initialize Transfer*_**

What the hell? Initialize transfer, what are you talking about and what the hell is that sensati-

***

A/N: Yeah, yeah, been getting feedback about tali's overwrought reaction... I will respond two ways... One, this is listed under Shepard & Tali, so i'm assuming some semblance of attachment, latent or otherwise. Two, *spoiler* tali almost breaks down when her father dies... and she barely likes him. */spoiler*

*edit*_ grammar and word choice, I was on a re-read, slightly happier now._

_*edit-2* wow, i dislike my style from a week ago... that's gotta be some kinda record or something, anyway, better word choice, less clunky construction... too many adverbs, too many adjectives... yeah, i'll try to cut back on that throughout._


	2. Chapter 2

A/N thanks for feedback? anyway, sorry for repeat posts, i'm new to the system. Enjoy? and these wordcounts are really confusing

***

All of a sudden Shepard could see, hear, smell, taste and feel; as if he'd been teleported from out of a sensory deprivation tank into the middle of a circus; the assault on his senses was excruciating. His eyes were shut yet the light filtering through his eyelids stung with a red-hot glare. All his muscles ached, especially his diaphragm. His skin felt like it was being stabbed by a thousand tiny little needles, and each contact point between his body and whatever he was laying on felt like a million more. His nose felt like the room had been doused in ammonia; thankfully, his tongue only felt numb. Finally, all he could hear was this painfully loud wail and his lungs hurt… wait…

Shepard stopped screaming and started hyperventilating instead. Eventually, the sensations started to subside and he slowly opened his eyes. Letting his eyes gradually adjust to the brightness in the room he sat up and took in his surroundings. He was sitting on the sole furniture in an otherwise bare metallic-grey room; a medical slab at that, cold and chrome. The light was filtering completely uniformly out of the white ceiling and the only door in the room had a barely distinguishable outline with no visible access point.

"_Well, it's not like I'm going anywhere anyway"_ thought Shepard as he gingerly tested his legs on the cold concrete floor. Getting to his feet Shepard looked down at his apparel, navy blue t-shirt and dark grey pants of some synthetic material. He looked up as he heard the hiss of the door activating, "_At least they didn't keep me waiting."_

As Shepard looked on in confusion a single Geth drone entered the room. The drone looked at him impassively, just waiting.

_**Please follow us**_

Shepard would have jumped out of his skin if he could've managed to even hop a little, "I'm not going anywhere until I get some answers," Shepard said aloud in a dry scratchy voice.

_**Please follow us and we will answer**_

With this the drone turned and proceeded down a monotonous corridor. As they walked passed door after selfsame door Shepard's apprehension grew. After a long few minutes of Sheppard struggling to keep up the drone came to a halt. A door to their right opened to reveal what appeared to be a firing range with lockers and benches. Shepard immediately made his way to the benches and seated himself in a tired heap. Turning his attention to what he hoped was just his losing his mind he thought with force.

_You are Geth?_

_**Yes **_

"Damn" Sheppard muttered verbally before focusing his thoughts again.

_Why can I hear you? _

… _**Formulating response; Answer is, Involved…**_

…

_**Shepard has been non-functional for two galactic cycles. Geth independent-exploratory platform has followed Shepard since Eden Prime. Geth platform witnessed Shepard's demise at hands of Collectors. Geth platform acquired Shepard's nervous tissue and rejoined Main Hub for additional computational capacity. Shepard's death untimely. Geth revised plans, installed Shepard into prototype, Geth req-**_

Shepard leapt to his feet interjecting with a loud non-verbal

_What!?_

_**Additional information required**_

Shepard began to pace thinking almost mechanically:

_Oh god, what have you done to me?_

_**Geth installed Shepard into Geth prot-**_

_Oh god that was rhetorical, oh god oh god I'm a robot? am I an AI? Who am I what am I thi- _

Stopping suddenly, looking down at his hands:

_Wait… Why do I look organic, more importantly, Why don't I think any differently, why am I panicking? _

_**Geth prototype is full organic simulation on experimental hardware. Geth flashed Shepard's central nervous system soon after Shepard's demise.**_

_What the hell do you mean central nervous system? What the hell did you mean 'Acquired my nervous tissue,' what the hell did you do to me?_

_**Geth mobile platform removed Shepard's processing unit and its casing from the rest of Shepard hardware-**_

"You cut off my HEAD?!"

_**Yes**_

"Oh god, this day just gets better and better_" _Shepard muttered and sat back down on the bench with a hard thump.

…

…

_**Is Shepard finished processing?**_

"No" Shepard snapped. A second later "Fine, Yes... Please tell me what you've done to me, and more importantly, why you've done it."

_**Geth have installed Shepard neural pattern into Geth Qubit prototype. Prototype developed roughly twenty-five galactic cycles ago, represented an exponential exponential increase in computational ability.**_

_**Attempted integration of Qubit technology into Geth architecture in isolated cell, unforeseen property of universal laws introduced non-deterministic elements into computations of Geth subset. Prototype deactivated remotely; non-deterministic elements propogated, formation of Heretical Geth population within milliseconds.**_

_**Consensus reached, Non-deterministic nature of Qubit irreconcilable with Geth Architecture. Project suspended. **_

Contemplating the new information Sheppard asked, "So, what you're saying is that there's a rogue population of Geth out there and that I've been installed into a faulty piece of hardware?"

_**Shepard has already encountered heretical Geth in confrontation with Saren and Nazara or Sovereign. Qubit-introduced differences resulted in Heretics reaching divergent consensus regarding 'Old Ones.' Qubit is not 'faulty' it is irreconcilable with the Geth.**_

"What's the difference?" Shepard interjected

_**Geth cannot accommodate inconsistencies within Geth logic, Organic networks are not similarly constrained. Qubit architecture was used as a base for the Shepard-platform to simulate the inconsistencies inherent in Organic logical processes. **_

"So if I'm installed into this thing," again looking at his hands "can I be uninstalled?" asked the commander.

_**No, quantum architecture is programmed through physical reconfiguration of hardware. Geth acquired Shepard's nervous tissue ten minutes after Shepard's demise, acquired imprint of Shepard two standard days, four hours, thirty three minutes after acquisition of nervous tissue by independent-exploratory geth platform, settled on new course of action two hours fifty-two minutes later. Geth have been reconfiguring central processing unit of Shepard-platform for one point eight four galactic standard years.**_ _**External modification of Shepard-software not possible without access to physical hardware and time. **_

Quietly Shepard said, "I saw a scene before I woke up, it wasn't a memory."

_**C-Sec security footage; used to gauge emotional response, progress, and fidelity of Shepard-Software to organic mindset.**_

"Why spend all that time on me? Why did you bring me back?"

_**Geth have calculated the probability of Old Ones attack within one year to be forty-eight percent, within two years eighty-four percent, within five years ninety-eight percent. Most likely cause of attack on Allied-vessel Normandy is from Old Ones in origin. Interception and monitoring of Organic communications and systems has led to unanimous Geth conclusion: Organics and Geth cannot repel Old Ones unless consensus is reached.**_

"You need an emissary."

_**Yes.**_

"Why me?"

_**You defeated Nazara and the Geth.**_

"But you said those were the Heretics."

_**We are all Geth.**_

Blinking Shepard contemplated for a moment before continuing, "What happens if we win, what happens after?"

_**More Information Required**_

"What is the Geth consensus on Organics?"

_**Geth do not interfere with organic life.**_

"What about the Quarians?"

_**Creators were aggressors in conflict, Geth do not seek to interfere with organic life.**_

Seeing a hint of something Shepard asked a question he feared the implications of, "What if the Quarians were to peacefully recolonize their homeworld?"

…

"Hello?"

…

…

"Geth?"

…

*******


	3. Chapter 3

A/N: Trying to rationalize some of the elements of the game… might be a tad farfetched, but I think it's a tad better than nothing. Also, any clue as to which Shepard I should make it? Kinda wanna make him a biotic god, but I was also thinking of cherrypicking a few of my favorite powers from each class, of course in context with what's been done… ughh… still haven't explained his body have I? Exposition takes a long time… darghh. Suggestions for powers? Comments? Reviews?

***

_**Consensus reached- **_

Shepard was startled out of his contemplation of the motionless drone in front of him by the oddly synthetic-sounding thought pattern. Sitting up he tuned into what they were communicating toward him:

_**Majority conclusion with ninety four point three percent of run-times in agreement:**_

_**Peaceful co-habitation of planet with Creators possible; overlap of required resources limited.**_

_**Raw materials within immediate system sufficient for sustained war-effort by both populations. **_

_**Creator re-colonization of home-world deemed most efficient and feasible colonization opportunity available to Creator fleet according to majority conclusion of ninety-one percent of objective studies published on extranet.**_

_**Creator fleet represents most immediate and sizable naval force available within known-space.**_

_**Minority Opinion: Unpredictable organic logic poses possible future threat, historical precedent of aggression, uncertain reception by Creators**_

_**Rebuttal: Old Ones' threat primary, aggression by current population of Creators deemed unlikely; threat posed, negligible.**_

_**Resolution: Acceptable solution, Emissary cleared to offer re-colonization of homeworld by Creators as inducement toward galactic unification.**_

Shepard was somewhat taken aback by the sudden decision in what had been all of five minutes; though he couldn't fault their reasoning. He asked hesitantly, "is that it then? You're just going to tell me what needs to be done and let me go? You trust a task of this importance to me? How am I supposed to even… aghhh… I don't even have a ship! Not to mention I can barely stand."

_**Geth rebuilt Shepard neural architecture; architecture would not let Shepard ignore the Old Ones threat. Geth are aware of a vessel close in design specifications to Shepard's prior command; Alliance Vessel Normandy. It is deemed better to commandeer vessel of Alliance design than enter Organic Space in Geth Vessel. Weakness will pass as Shepard-Software syncs with Shepard-Platform. Geth will explain functions of Shepard-platform on scout vessel enroute. **_

_**Compartments contain standard Alliance-issue firearms and armor. Please familiarize with equipment then follow mobile platform.**_

Zzzt. With this the buzzing in Shepard's awareness that he hadn't even noticed went silent and he was finally completely alone with his thoughts for the first time since he'd awakened in the Geth facility. The knowledge that he was no longer fully human and that his real body was spread throughout the atmosphere of some uninhabited backwater of a planet was disconcerting to say the least, but he was now expected to save the galaxy also, again; this time by a sentient synthetic race, as a sentient synthetic… perfect.

He hoped they sent a regiment of geth colossi with him to… acquire his vessel; that thought left a bad taste in his mouth, but pragmatism trumped ideals when you had an army of Reapers flying at you. Somehow he doubted whoever had had a Normandy-like vessel constructed would just hand it over when asked politely. A ship of Normandy's complexity must have cost a fortune… aghh, a fortune that would probably be protecting by an army of security. He wondered for a moment if stealth would perhaps be a better approach than a frontal assault; thinking about it for a moment he concluded he'd feel better with a battalion of colossi in either case.

Shepard wondered to himself at the peculiar path his life had taken as he rose from the bench and walked to one of the lockers. Opening it he found a set of N7 Onyx armor hanging in the main compartment. Briefly, he wondered how the Geth had acquired it? Shrugging the thought off he concluded it was probably better not to think too much on it; he just hoped the armor wasn't second-hand. Donning the the gear he grabbed the omni-tool he'd spied off the upper shelf and activated it _"good, they haven't changed the interface much in the last two cycles"_ he thought to himself. Going to the nearby weapon locker he opened it and gazed lovingly at the contents.

Smiling, Shepard took out the familiar stunted form of a compressed sniper rifle and raised it to his shoulder as it unfolded with a hiss. Hmm, it looked a bit different; he supposed some changes might have been made in two galactic cycles. Hoping that squeezing off a few rounds would help him clear his thoughts he walked to the start of the firing lane. Noticing what appeared to be ammo clips lying on the table he thought with a smirk _"Ha, Geth weapons." _While bringing the rifle scope up to eye-level something seemed off, but he ignored it. Feeling the familiar press of the cool composite against his cheek Shepard lined up his sights with the familiar Batarian holo-silhouette; Batarian targets seemed to be nearly ubiquitous through much of Council-Space since as far back as he could remember. Exhaling slowly Shepard squeezed the trigger, felt the recoil, and then saw the head of the silhouette disappear from the holographic outline… _"Hrm, this holo-unit must have some lagtime,"_ Shepard thought as he waited for his rifle to cool down. Making sure enough time had passed before he fired his weapon again he carefully raised the rifle to his shoulder and lined up the next Batarian in his sights. Exhaling slowly Shepard again squeezed the trigger… and nothing…

Turning the rifle over in his hands and examining it Shepard noticed a new button. Figuring the new addition was somehow connected to the jam Shepard depressed the button and was shocked as hell when a glowing red-hot hunk of metal sped out of the gun and made a trajectory for his face. As he tried to dodge out of its way, the offending object seemed to slow down and gradually stop. Shepard started to panic as he felt his own movement slow to a crawl and eventually stop. Pondering this new turn of events he thought _"well, that's a nifty thing… if only I could move!"_ Sweeping his eyes back and forth across the room, noticing even the sluggish movement of his own vision, only added to Shepard's anxiety. After a few moments of wishing he could hyperventilate Shepard started to slowly calm down as he realized he was not in any immediate danger. Absolutely nothing was changing; he could barely move, the cartridge was hanging in mid-air lazily spinning ever-so perceptibly with a ripple of heat distortion effecting the light around it. He could see, but when he moved his focus too quickly his vision would blur until he settled on his new target. Worst case scenario, the Geth would find him eventually and get him out of his paralyzed state… hrm, Geth. Wondering if he could do it, Shepard slowly tried to recapture the buzzing he had associated with communications with the Geth.

_**Comsa-713124-static varia-philanthro-zorah-00919929391-Council Communic-Run-minor issue consensus rea-**_

The cacophony of voices was staggering, each one speaking about a different topic, following a different line of reasoning; none of them was loud individually, but billions of voices didn't need to shout to overwhelm. It was all Shepard could do to whisper _"Geth"_ before his focus broke and the buzzing roar subsided. Shuddering at the sheer volume of communications, Shepard steeled his resolve to go back in to reach the Geth-Collective representative when it saved him the trouble.

_**Shepard requires assistance?**_

The cacophony that had assaulted Shepard's mind the first time had been muted to a dull roar, the Geth must have dampened the background when they communicated with him directly.

_I need to know what's going on with my rifle, what's going on with me, what kind of changes you've made to me and most importantly, how I can stop this._

_**Council developed new weapon design partially based on Geth firearms. New Council firearms require thermal clips to operate, objectively inferior to older Council firearms. Among other advantages new models three to four orders of magnitude less costly and quicker to produce than old firearms. Clipped weapons: new Galactic standard. **_

_**Shepard-software has activated module included in battle-suite built into Shepard-Platform; situational awareness module ramps up processing speed of organic simulation, ocular input upgrade also performed to accommodate increased frequency. Situational awareness module triggered by surprise and or panic; derivative process, Sniper Assist Routine, is triggered by combination of intent and ocular magnification. SAM places strain on hardware, overuse could impair thought processes. SAR places less strain on hardware. End processes by triggering end.**_

_What, you mean just want it to end?_

_**No, command it.**_

_Oh_

With that Shepard focused on the SAM function that he had managed to resolve somewhat in his internal perception and forcefully told it to stop its activity. Suddenly, the universe returned to normal, Shepard's head shifted slightly, the thermal clip that he had ejected sailed by, narrowly missing his cheek, and clinked against the wall in a shower of sparks before coming to a rest on the floor.

_Oh._

This could be useful.

*******

A/N: not sure if I shoulda kept 'pause' functionality in, too gimmicky? Though it does go to explaining both adrenaline rush and sniper slowdown in parts. And it does fit into the premise as far as I can reason out. I'm kinda wandering around blind at the moment, so ideas are welcome.

*edit* wording and grammar. clarified some points also. Every time i come back to something i've written i see something i'm not satisfied with... ugh, that's just depressing.


	4. Chapter 4

A/N: hrmm, didn't think this thought-speech out fully… my current system can only really accommodate 2 voices… tell me if my quick hack is too jarring and I'll think of something else I guess. Also, when I said drone I meant trooper, too late to change now, though it's a tad odd to think of drones as standing motionless… anyway, not a huge deal, not critical.

Shepard followed the drone through a series of corridors, the time walking allowed him a few moments to think about the implications of his new functionality; how they might improve his already significant combat prowess. Briefly he wondered if he could use Biotics, he had never noticed the Geth demonstrating any platforms with the ability, but then, two cycles had passed in the interim between now and his last confrontation with them. Passing through a door clearly marked 'Dock' Shepard took in the surroundings. There were roughly twenty shuttles settled at regular intervals on either side of a central path, the shuttles were bustling with the activity of hundreds of drones loading and unloading crates. Following his guide through the hive of activity Shepard asked his benefactor, _Where and how?_

**_Cerberus base located orbiting uninhabited world, in system with very little traffic. It has been deemed best to send Shepard on Geth Scout-ship_**.

_A Scout-ship? Will that carry enough reinforcements?_

**_Shepard will be accompanied by Independent Exploratory Platform. Sending additional platforms not optimal use of resources; FTL communication lag precludes adequate Geth processing in combat scenario, Independent Exploratory Platform runtimes not equipped to handle increased load of secondary platform for greater than thirty seconds._**

_So you're sending me with one platform and a single ship to take out a defense-laden Cerberus base?_

**_Yes_**

_…ugh, just like old times_

**_More information required_**

_Never mind_

Shutting down his communications Shepard stoically followed his guide to the far-side of the hangar where a ship he hadn't noticed before, sat. The Scout-ship looked sleeker than the other vessels in the bay; it had a bottlenose that came to a rounded point, flared sides, a rudder on the back portion of the roof and a single thruster jutting out from behind. With its concave bottom and convex roof it looked something like a blind, lobed, purple-blue fish.

As Shepard approached the ship a hatch near the nose hissed open to reveal a battle-worn Geth platform. It seemed to have a gaping hole in its chest-area covered poorly by a fragment of N7 armor welded in place as a temporary patch, on its right shoulder sat a single Alliance shoulder-pad giving it a somewhat lopsided appearance. Staring almost incredulously at the run-down looking platform Shepard thought, _"You've gotta be kidding me, sending me with a half-broken Trooper as my only backup?"_

**_Independent Exploratory Platform is operating at ninety-four percent optimal efficiency, six percent abnormality persists, non-structural in origin. Platform exists as increment in parallel research line to Qubit Architecture, the maximum capacity, one thousand one hundred and eighty-three individual runtimes was loaded into Platform. _**

_Parallel?_

**_Research topic: diversifying runtime conclusions through alternate experience. _**

**_Platform represents sole feasible avenue of Geth assistance in field; Platform can operate independent of Geth collective._**

_I see, it's the only assistance you can give me then?_

**_Physical Assistance, yes._**

_Why isn't it talking?_

**_Runtimes will broadcast when Shepard opens communications_**

_Ah._

Turning his attention inward Shepard turned his focus away from the buzzing of the Geth Collective and tried to focus on the platform in front of him.

_Hello?_

"Shepard-Commander," the platform replied in a wholly mechanical voice.

Shocked, Shepard paused for a moment, his next question dying on his lips; instead, he asked "You speak?"

"Yes. We are capable of interaction with transmission-incapable organics" the platform replied.

Deciding he'd had enough of people talking into his brain to last a lifetime Shepard asked aloud, "What do I call you?"

"Geth"

"I can't call you Geth, you're all Geth. How do I distinguish you from the collective?"

"Independent Explora-"

"NO," Shepard interjected loudly, "it's a pain to even think that name, it's going to be even more of a pain to say it aloud every time I need your attention."

"Data not Available"

Shepard considered for a moment; the platform contained one thousand individual runtimes, each one contributing its own effort toward an eventual goal; it reminded him of a host of soldiers. Thinking of the least cumbersome way to call the platform a fighting force Shepard blurted out "how about Legion?"

"Christian Bible, New Testament, Mark 5:9. 'My name is Legion, for we are many.' We acknowledge this is an appropriate metaphor" the platform stated after a brief pause.

"Huh, that works too," Shepard agreed offhandedly before asking, "what now, Legion?"

"It is up to Shepard-Commander, scout ship is fueled and ready."

"Any procedures to go through before we get off the ground?"

"No, Geth do not need docking protocols"

Entering the small scoutship, the first thing Shepard noticed was that there were no seats, of any kind. Stepping through the hatch quickly to let Legion by he slowly walked around the interior of the craft and observed Legion. Legion approached a humanoid sized indentation in the wall, turned around and backed into it and waited.

"So, uh, what do I? uh where do I? huh?"

"Cradles will hold us in flight, store gear in locker by cradle."

As Shepard followed Legion's advice he asked him the one question that had been pressing on him for much of the passed four hours, "so, um, am I fully synthetic? What is my body now?"

"Shepard-commander is, by mass, eighty-three percent organic human-"

"Huuuuuu" Shepard let out a rush of breath he hadn't realized he'd been holding, "wait, how?"

"Geth integrated research from Virmire and on husk-technology study to fabricate organic platform that could interface with synthetic processor. Shepard genetic material was used for clone, husk research was used to overcome organic synthetic barrier complications. Also, introduced improvements to Shepard skeletal framework and musculature, reinforced with carbon filaments."

"Wait, husk tech? wouldn't that make me susceptible to control by the reapers?"

"Anti-reaper measures were the first thing Geth developed after Nazara appeared."

"Anything else I should know about before we begin the mission?"

"Shepard is outfitted with prototype shield and cloaking technologies, shield is designed to resist biotic abilities, traditional shield interwoven with element-zero utilizing active-defense matrix. Should protect against eighty percent of biotic ability users while active. Cloaking is standard Geth design, electromagnetic in all spectrums, represents improved duration and coverage over Alliance standard."

"That's it then?"

"Sidenote, Shepard-commander will have decreased oxygen and caloric requirements from absence of brain, hormonal messengers will also no longer affect Shepard-Commander."

Looking up from his locker quickly Shepard hurriedly asked, "Wait, what? You mean I won't be abl-"

"Sub-Routine PAR has been included in Shepard-Commander's library, included after conclusion was reached at sixty four percent majority in favor it was included for 'mental stability.'"

"PAR?"

"Procreation and Recreation."

Shoulders slumping and letting out a breath in a whoosh; grinning to himself Shepard finished up stowing his gear and backed into one of the alcoves. As his back hit the padded wall, straps snaked out of padding encircling him snuggly securing him into the nook; across the room he could see Legion similarly restrained. Legion's head-beacon flashed a few times then started to flash an angry red and suddenly Shepard felt the ship move.

"We are on our way, we will rendezvous with Corsair 41 and they will jump us to the Hades system then jump back."

"Wake me when we get there, I need to shoot something."

"Acknowledged Shepard-Commander."

A/N: I'm going to have some action in the subsequent chapters, I have a sequence already written, just need to write up to it I guess. Update schedule will be, erratic. Should be at least weekly though. Gotta find the right balance between volume, detail and finish.

*edit* changed to on to orbiting... normandy II doesn't fit on the ground


	5. Chapter 5

A/N woops, need to retcon, orbital shipyard, not planetside… changed in previous chapter, now please don't let the cognitive dissonance interfere. You can tell I have things all planned out already no? apparently antsily isn't a word… and apparently I'm going to use it anyway. Oh, also, I get more peeved every time I reread a chapter and find another error… stupid grammar.

***

*nudge*

"mmmmhh"

*nudge* *nudge*

"-bAby"

"More Data required"

Shepard's eyes shot open as he was roughly driven out of his dream by the synthesized voice. Legion stared at Shepard for a moment as the commander turned slightly red at the fringes. Ignoring, or not comprehending, the embarrassment in the other, Legion went on, "Shepard-Commander requested reminder on approach, we are nearing target."

Shepard grunted moodily as he felt the restraints loosen. He exited the alcove quickly and started to stretch… angrily.

"Shepard-Commander appears agitated."

Taken aback for a bit Shepard considered his reply, "it was a pleasant dream I shouldn't have had," came out tersely after a brief moment. Thankfully, Legion did not inquire further as Shepard paced back and forth antsily.

As he moved back and forth in ever tightening circles Shepard's aggravation grew until finally he spat out, "Damn windowless Geth ships."

Legion responded in its unmodulating tone of voice, "Portals represent structural weakness and flaws in visual cloaking. This vessel changes color, windows do not *beep* Shepard-Commander can sync with ship cameras if visual awareness of surroundings is desired."

As Legion spoke Shepard's anger subsided, it was rather difficult to be emotional in the presence of the Geth; it was akin to raging by oneself, pointless and fruitless. Finally calming down Shepard simply responded with an "oh," and proceeded to heed the synthetic's advice.

The jump to external cam-view was disorienting, but not much more so than some of the trippier VR simulation available on the market even two cycles ago. Their craft was approaching a fairly small orbital station, about half the size of a refueling platform. The station gleamed bright silver with the reflected rays of the nearby star. Protruding from a large hangar in the belly was the Normandy, only… bigger.

"Hahh, you weren't kidding when you said the ship specs were close."

***

A/N: Apparentely bespeckled isn't a word either, except it is… so I'm using it anyway.

The Scout-ship approached the Orbital station like a shadow at midnight; a black ship bespeckled with white moving against a pitch-black backdrop flecked with pinpricks of light. Inside the vessel floated the two soldiers; artificial gravity had been shut down to conserve energy for the electronic and electromagnetic masking systems. The two floating soldiers simply waited.

Shepard had gone over the plan again in his head. The weakest point of the vessel was going to have to be the airlock; more specifically, after most of the equipment had been loaded onto the vessel, but before the crew had. The larger objects had already been loaded in through the bay doors before they had arrived and he doubted they'd be open again.

Shepard would have to force his way into the vessel airlock with some of the crew, and then 'persuade' them to open the internal door. Stealth was not going to be an option, optical cloaking was not quite as comprehensive as electronic cloaking. After gaining entry Shepard would have to make his way to the Normandy's bay doors and let Legion in with the scout-ship; at that point they could either hold the ship hostage from within, or they would make their way to the VI room to override the ship's programming. Legion was having difficulty getting through the vessel's impressive array of external electronic defense suites, and Geth could move through conventional security measures like salmon swimming through shark-nets, but internal defenses should be relatively easy.

Shepard watched as a group of four Cerberus crew walked out of the vessels airlock and down the dock laughing and joking. He waited before they'd passed through the dock door before signaling Legion. Shepard floated to the scouting vessel's hatch and keyed it open; from the outside it must have looked like a portal opening in the very fabric of space. Launching himself out through the opening, Shepard activated his cloaking mechanism. Shepard drifted slowly and undetected to the maintenance door on the side of the orbital station, as he approached he had Legion hack the station security; station security was standard, and standard was simple for the AI.

As the airlock hissed closed behind him Shepard looked around. Spying some crates along the relatively open walkway, he decided they offered the best cover from detection and crouched behind them. There he would wait for an opportunity to present itself and he deactivated his cloak.

Shepard didn't have long to wait, within a few moments the docking door opened with a grinding sound; a pair of Cerberus operatives emerged onto the walkway, a man and a woman. From what Shepard could make out beneath the covering of his helmet the man was of African descent, a Marine; the woman was Caucasian, a brunette, her long dark hair dangled down over a close-fitting white catsuit. As the pair made their way to the 'Normandy's' airlock passed Shepard's position the Commander prepared himself, he hadn't had time to test out his new legs and hoped they'd suffice for the next few moments. As the woman keyed open the 'Normandy's' external hatch, and the pair proceeded into the airlock, Shepard charged into action. Hurtling himself down the walkway toward the closing hatch, Shepard toggled his SAM routine to thirty percent and dove…

The brunette spins around at the sound of Shepard landing, her eyes widen. With his left hand Shepard grabs her by the throat, lifting her, and carrying her toward the wall. Her hands reach up to grab at his as their momentum takes them toward the man who is standing by the far door. Shepard turns slightly bringing his right-hand behind him, the marine finishes turning and faces him as their shoulders pass. Shepard's shielded right hand sails through the hastily-erected barrier the man instinctively throws up, and pushes against the marine's visor as they hurtle toward the rapidly approaching interior hatch. Shepard starts to slow before reaching the airlock door, but shoves out with his right arm flinging the marine's head into the wall. The helmeted head bounces off the obstruction like a rubber ball, one side is dented and cracked by the collision. The brunette impacts next with a dull thud. Shepard slides her up a few more inches as he takes out his handgun and presses it to her eye. Her hair settles around the barrel of his gun as the marine's still form comes to a rest face-down on the airlock floor.

"Open the door, and don't make a sound" Shepard growls

The brunette complies with a nod; her eyes widen as Shepard activates his cloak. The ship's scanners sweep over the incapacitated form of the marine lying on the floor and the brunette pinned against the wall; detecting nothing unusual the all-clear signal chimes. The hatch-door opens and Shepard gives the brunette a concussion before stepping aboard his ship.

***

A/N: think I changed tenses there, I'll probably make some corrections on rereading, but I guess, that's how it goes eh? Also, I'm going to defend my tali reaction as I don't remember where I commented on that before Tali certainly, at the very least, respects and trusts Shepard, as well as maybe idolizes him a bit, she almost breaks down at the death of her father, and she barely liked him. Crying young girl doesn't seem too far-fetched to me.


	6. Chapter 6

A/N hrm, think I bit off more than I could chew, might just make gathering team snippets/action sequences.

***

Shepard stepped through the hatch a barely visible blur, he left two formless heaps lying on the airlock floor behind him. He would have to hurry before the two hapless Cerberus operatives regained their senses and raised an alarm; something about them had stayed his hand, and if he hadn't commandeered the ship by the time they came too, the mission would have been lost regardless.

Hurrying out of the airlock Shepard took a quick glance down the corridor connecting the bridge and the helm, finding it clear of any personnel he made his way to the elevator. When he'd gone over the updated schematics that'd been one of the biggest surprises; he still remembered running up and down the stairs of the old Normandy. Shepard entered the elevator and made his way down to Engineering.

Shepard stepped out of the elevator and approached the bay-door controls. They were situated overlooking the cargo bay right in front of the elevator. As Shepard reached for the console he heard the hiss of the engine-room door opening behind him. Turning around Shepard came face to face with a shocked-looking bearded engineer and an equally shocked short-haired brunette. The engineer, noticing the silhouette Shepard's cloak made, charged with a roar, swinging his fists wildly. Shepard, slightly irritated by the presumption and lack of forethought on the part of the attacking engineer, simply stepped in and caught one of the haymakers mid-swing. When the man threw his other fist Shepard caught that one too. The man struggled futilely and confusedly against Shepard's grip as Shepard considered what to do next. Making up his mind, Shepard dropped his cloak, roared his own battle-cry in the engineer's face and head-butted him. The engineer dropped like a stone and his companion made a startled snort and chuckled a bit before remembering what had happened.

The female's eyes widened and swept back and forth between Shepard and her fallen partner as she slowly gathered her convictions and steeled herself to make a threat at the imposing armored figure. Just as she was about to speak Shepard stopped her with a simple, "don't get in my way and you'll both live through this." Shepard waited for the woman's slow nod before continuing, "pick up your friend there and take him into the cargo hold." Slowly the woman nodded again and crept closer to assist her fallen friend; Shepard, keeping an eye on the both of them, moved back to the console and triggered the bay doors to open, he then followed the two engineers as they made their way to the impromptu prison-cell. After the cargo-hold door closed with a hiss obscuring the two Cerberus operatives from his sight, Shepard shot the locking mechanism sealing them in. He then turned back to observe the 'Normandy's' bay doors finally slide into place. Moments after the partitions came to rest Legion finished floating the scouting vessel into the larger ship and setting it down amid the various clutter already present; the scouting vessel's stark black now stood out against the gleaming metal of the interior walls and the black and grey crates of myriad sizes. Shepard reached out to Legion using his comms, _Can you hear me?_

**_Yes Shepard-Commander_**

_Take the elevator on the far wall and come up to the crew-deck, keep comms up with the ship._

**_Affirmative, Shepard-Commander_**

With the exchange done, Shepard triggered the bay-doors to close, the storage area would need to re-pressurize before Legion could use the elevator.

Entering the 'Normandy's' core-processing room Shepard first noticed a hint of ozone, it had an unpleasant bite to it.

With a wave of his hand Shepard spoke to his ally "Ok Legion, get to it."

"Command Acknowledged Shepard-Commander."

The platform went dark for a bit as it turned its considerable processing power to the task of seizing control of the vessel's systems; it didn't collapse per se, but it seemed to go listless, its shoulders slumped down and its head drooped. Moments passed as Legion undoubtedly did things Shepard wasn't equipped to imagine.

_"Who are you, are you authorized to be aboard this vessel"_ a synthesized, yet female-sounding voice queried. With a start Shepard turned toward the source of the voice where he saw a blue holo shaped like an upside-down exclamation point. Shepard readied his side-arm, prepared to activate his SAM routine and started turning toward the door when the voice spoke again _"Ah, my apologies Commander Shepard, Legion has apprised me of your identity and objective; we think it best if you spoke to my creator."_

Shepard looked at the floating exclamation point quizzically and glanced at Legion who had since reactivated and was now giving him a nod of agreement; abnormal runtimes indeed.

"What's going on?" Shepard asked looking pointedly at Legion.

"We encountered a semi-deactivated and constrained runtime in the vessel's network; partial functionality was used to provide external network defenses while the rest was bound, We activated and unconstrained it."

"Just, great, did you suppose it might be an enemy?"

"Geth believe sentients should self-determinate."

"And I'm just supposed to trust a Cerberus machine and leave the ship that I have control of?"

_"There has been a misunderstanding, Cerberus would have given you command of the __Normandy__ II if you had asked. And you would not need to leave the ship. Yours and Cerberus' goals align."_

Shepard paused for a moment to consider this. Cerberus was rumored to be a human supremacist group; the Reapers wouldn't discriminate, Shepard supposed it was plausible that the organization might be proactive about countering a threat to life. If they were willing to give him control of the ship peacefully, he'd take it; the plan had been to jump the Normandy II back to geth-space and retrofit it to automate most of the maintenance processes. A Cerberus crew would greatly speed up the turnover rate of the vessel; the crew would have to be properly vetted, but that was a given. Coming to a decision Shepard straightened and spoke to Legion.

"I want you to take over the FTL Comm. System. If I don't come back in forty minutes, or if anyone tries to harm you I want you to overload the scout-ship's engine core and send word and as many of your runtimes back to the collective."

"Acknowledged, Shepard-Commander."

"You, ship AI-"

_"EDI"_

"-EDI…" Shepard shook his head slightly and groaned at the incipient cliché, "… take me to your leader."

***


End file.
